Genetic Variant ENST00000323078.7:c.-413G>A (chr7-150323292-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000323078.7(LRRC61):c.-413G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 258,264 control chromosomes in the GnomAD database, including 7,364 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.19 ( 3506 hom., cov: 33)

Exomes 𝑓: 0.27 ( 3858 hom. )

Consequence

LRRC61
ENST00000323078.7 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.46

Publications

24 publications found

Variant links:

Genes affected

LRRC61 (HGNC:21704): (leucine rich repeat containing 61) Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

LRRC61 links:

ACTR3C (HGNC:37282): (actin related protein 3C) Predicted to enable ATP binding activity. Predicted to contribute to actin filament binding activity. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACTR3C links:

ENSG00000293476 (HGNC:):

ENSG00000293476 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000323078.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ACTR3C	NM_001164458.2	MANE Select	c.-52+177C>T	intron	N/A	NP_001157930.1
LRRC61	NM_001363433.1		c.-315+80G>A	intron	N/A	NP_001350362.1
LRRC61	NM_001363434.1		c.-314-2549G>A	intron	N/A	NP_001350363.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
LRRC61	ENST00000323078.7	TSL:1	c.-413G>A	5_prime_UTR	Exon 1 of 2	ENSP00000339047.6
ACTR3C	ENST00000683684.1	MANE Select	c.-52+177C>T	intron	N/A	ENSP00000507618.1
ACTR3C	ENST00000478393.5	TSL:1	c.105+177C>T	intron	N/A	ENSP00000417426.1

Frequencies

GnomAD3 genomes

AF:

0.190

AC:

28832

AN:

152116

Hom.:

3513

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0456

Gnomad AMI

AF:

0.389

Gnomad AMR

AF:

0.146

Gnomad ASJ

AF:

0.320

Gnomad EAS

AF:

0.289

Gnomad SAS

AF:

0.274

Gnomad FIN

AF:

0.246

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.255

Gnomad OTH

AF:

0.183

GnomAD4 exome

AF:

0.266

AC:

28218

AN:

106030

Hom.:

3858

Cov.:

AF XY:

0.265

AC XY:

15685

AN XY:

59116

show subpopulations

African (AFR)

AF:

0.0696

AC:

AN:

474

American (AMR)

AF:

0.155

AC:

196

AN:

1262

Ashkenazi Jewish (ASJ)

AF:

0.341

AC:

715

AN:

2098

East Asian (EAS)

AF:

0.370

AC:

143

AN:

386

South Asian (SAS)

AF:

0.273

AC:

7085

AN:

25986

European-Finnish (FIN)

AF:

0.260

AC:

1934

AN:

7436

Middle Eastern (MID)

AF:

0.228

AC:

AN:

400

European-Non Finnish (NFE)

AF:

0.267

AC:

16701

AN:

62634

Other (OTH)

AF:

0.247

AC:

1320

AN:

5354

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.529

Heterozygous variant carriers

959

1918

2877

3836

4795

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

128

160

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.189

AC:

28814

AN:

152234

Hom.:

3506

Cov.:

AF XY:

0.191

AC XY:

14254

AN XY:

74436

show subpopulations

African (AFR)

AF:

0.0456

AC:

1894

AN:

41572

American (AMR)

AF:

0.146

AC:

2238

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.320

AC:

1112

AN:

3470

East Asian (EAS)

AF:

0.288

AC:

1485

AN:

5156

South Asian (SAS)

AF:

0.274

AC:

1322

AN:

4832

European-Finnish (FIN)

AF:

0.246

AC:

2609

AN:

10596

Middle Eastern (MID)

AF:

0.228

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.255

AC:

17350

AN:

67982

Other (OTH)

AF:

0.181

AC:

382

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1198

2397

3595

4794

5992

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

318

636

954

1272

1590

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.229

Hom.:

748

Bravo

AF:

0.173

Asia WGS

AF:

0.262

AC:

913

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

8.9

(source)

DANN

Benign

0.82

PhyloP100

2.5

PromoterAI

0.31

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over